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Browsing Center for Genomic Regulation (CRG) by Author "Radusky, Leandro"

Browsing Center for Genomic Regulation (CRG) by Author "Radusky, Leandro"

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  • FoldX 5.0: working with RNA, small molecules and a new graphical interface
    Delgado Blanco, Javier; Radusky, Leandro; Cianferoni, Damiano; Serrano Pubull, Luis, 1982- (Oxford University Press, 2019)
    SUMMARY: A new version of FoldX, whose main new features allows running classic FoldX commands on structures containing RNA molecules and includes a module that allows parametrization of ligands or small molecules (ParamX) ...
  • FoldX accurate structural protein-DNA binding prediction using PADA1 (Protein Assisted DNA Assembly 1)
    Delgado Blanco, Javier; Radusky, Leandro; Climente González, Héctor; Serrano Pubull, Luis, 1982- (Oxford University Press, 2018)
    The speed at which new genomes are being sequenced highlights the need for genome-wide methods capable of predicting protein-DNA interactions. Here, we present PADA1, a generic algorithm that accurately models structural ...
  • From research to rapid response: mass COVID-19 testing by volunteers at the Centre for Genomic Regulation
    Ghose, Ritobrata; Aranguren-Ibáñez, Álvaro; Arecco, Niccolò; Balboa, Diego; Bataller, Marc; Beltran, Sergi; Benisty, Hannah, 1986-; Bénard, Angèle; Bernardo, Edgar; Carbonell Sala, Silvia; Casals, Eloi; Ciampi, Ludovica; Condemi, Livia; Corvò, Alberto; Cosín Tomàs, Marta; Cuenca-Ardura, Mirabai; Duran Serrano, Juan Manuel; Espejo Díaz, María Isabel; Fernández Callejo, Marcos; Gañez-Zapater, Antoni; Garcia-Castellanos, Raquel; Garrido, Romina; Henkin, Gil; Hermoso Pulido, Antonio; Hernandez-Alias, Xavier; Herrero Vicente, Jorge; Ingham, Matthew; Lim, Wei Ming; Llonch, Sílvia; Marmesat Bertoli, Elena; Miguel Escalada, Irene; Montero-Blay, Ariadna, 1994-; Navarrete Hernández, Cristina; Neguembor, Maria Victoria; Ní Chárthaigh, Róisín-Ana; Pardo-Lorente, Natalia; Pascual-Reguant, Laura, 1990-; Pérez-Lluch, Sílvia; Perza, Reyes; Pesaresi, Martina, 1991-; Picó Amado, Daniel; Pifarré, Paula; Piscia, Davide; Plana-Carmona, Marcos; Ponomarenko, Julia; Radusky, Leandro; Rivero, Ezequiel; Rogalska, Malgorzata; Torcal Garcia, Guillem, 1991-; Wojnacki, José (F1000Research, 2020)
    The COVID-19 pandemic has posed and is continuously posing enormous societal and health challenges worldwide. The research community has mobilized to develop novel projects to find a cure or a vaccine, as well as to ...
  • PDBe-KB: collaboratively defining the biological context of structural data
    Varadi, Mihaly; Radusky, Leandro; Serrano Pubull, Luis, 1982-; Velankar, Sameer; PDBe-KB consortium (Oxford University Press, 2022)
    The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or ...
  • Protein-assisted RNA fragment docking (RnaX) for modeling RNA-protein interactions using ModelX
    Delgado Blanco, Javier; Radusky, Leandro; Cianferoni, Damiano; Serrano Pubull, Luis, 1982- (National Academy of Sciences, 2019)
    RNA-protein interactions are crucial for such key biological processes as regulation of transcription, splicing, translation, and gene silencing, among many others. Knowing where an RNA molecule interacts with a target ...
  • ProteinFishing: a protein complex generator within the ModelX toolsuite
    Cianferoni, Damiano; Radusky, Leandro; Head, Sarah A.; Serrano Pubull, Luis, 1982-; Delgado Blanco, Javier (Oxford University Press, 2020)
    Summary: Accurate 3D modelling of protein-protein interactions (PPI) is essential to compensate for the absence of experimentally determined complex structures. Here, we present a new set of commands within the ModelX ...
  • pyFoldX: enabling biomolecular analysis and engineering along structural ensembles
    Radusky, Leandro; Serrano Pubull, Luis, 1982- (Oxford University Press, 2022)
    Recent years have seen an increase in the number of structures available, not only for new proteins but also for the same protein crystallized with different molecules and proteins. While protein design software have proven ...
  • Using protein-per-mRNA differences among human tissues in codon optimization
    Hernandez-Alias, Xavier; Benisty, Hannah, 1986-; Radusky, Leandro; Serrano Pubull, Luis, 1982-; Schaefer, Martin H. (BioMed Central, 2023)
    Background: Codon usage and nucleotide composition of coding sequences have profound effects on protein expression. However, while it is recognized that different tissues have distinct tRNA profiles and codon usages in ...
  • VarQ: a tool for the structural and functional analysis of human protein variants
    Radusky, Leandro; Modenutti, Carlos; Delgado Blanco, Javier; Bustamante, Juan P.; Vishnopolska, Sebastian; Kiel, Christina; Serrano Pubull, Luis, 1982-; Marti, Marcelo; Turjanski, Adrián (Frontiers, 2018)
    Understanding the functional effect of Single Amino acid Substitutions (SAS), derived from the occurrence of single nucleotide variants (SNVs), and their relation to disease development is a major issue in clinical genomics. ...

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